# 🪄 napari-magic-wand
Object annotation in Napari using a *magic wand* (shortest path algorithm). This plugin is based on the [PyIFT](https://github.com/PyIFT/pyift) library. This tool supports annotation in 2D (grayscale and RGB), 2D+t (grayscale, frame by frame) and 3D images (slice by slice). It can be used to annotate **paths** or solid objects via their contour.
<p align="center">
<img src="https://github.com/MalloryWittwer/napari-magic-wand/blob/main/assets/screenshot.gif" height="400">
</p>
Please also take a look at the [grabber-ift](https://www.napari-hub.org/plugins/grabber-ift) plugin, which offers similar functionality but slightly different user interactions.
## Installation
You can install `napari-magic-wand` via [pip]:
pip install napari-magic-wand
## Usage
- Select the plugin from the `Plugins` menu of Napari.
- Open an image to annotate (2D, 2D+t, or 3D).
- Click on the button "Start live wire" or press `S`. A new `Labels` layer *Live wire (current edit)* should appear.
- With the *Live wire* layer selected, click on the image to annotate the contour of an object.
- Double-click to confirm the annotation path.
**Options and parameters**
- *Close and fill objects*: You can fill (or not) the inside of the annotated object. Do not tick this option if you are annotating **paths** (e.g. filament-like strucutres).
- *Auto-increment label index*: Tick this option to increment the label index every time a new object is completed (e.g. if you are annotating multiple objects).
- *Sigma*: Higher values of sigma increase the "stickiness" of the object boundaries to the magic wand.
## Contributing
Contributions are very welcome. Please get in touch if you'd like to be involved in improving or extending the package.
## License
Distributed under the terms of the [BSD-3] license,
"napari-magic-wand" is free and open source software
## Issues
If you encounter any problems, please file an issue along with a detailed description.
----------------------------------
This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
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